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Updated: Jun 28, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
pipesnake: generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci
Ian G Brennan1,2, Sonal Singhal3, Ziad Al Bkhetan4
1Natural History Museum, London, SW7 5BD, United Kingdom.
Motivation:
Phylogenetics has moved into the era of genomics, incorporating enormous volumes of data to study questions at both shallow and deep scales. With this increase in information, phylogeneticists need new tools and skills to manipulate and analyze these data. To facilitate these tasks and encourage reproducibility, the community is increasingly moving toward automated workflows.
Results:
Here we present pipesnake, a phylogenomics pipeline written in Nextflow for the processing, assembly, and phylogenetic estimation of genomic data from short-read sequences. pipesnake is an easy to use and efficient software package designed for this next era in phylogenetics.
Availability And Implementation:
pipesnake is publicly available on GitHub at https://github.com/AusARG/pipesnake and accompanied by documentation and a wiki/tutorial.
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